How to dump genes from GenBank in GFF3 format?

Question

[Dan]

If I look at this record in GenBank I see about 6k genes: https://www.ncbi.nlm.nih.gov/nuccore/CM000760?report=gbwithparts

I'd really like to be able to dump those genes in GFF3 format, but I'm guessing I can't do that in a single step, so...

1. How to dump all genes from a GenBank record in 'whatever' format?
2. How to convert 'whatever' format to GFF3?

[Pierre Lindenbaum]

duplicate of Any tools converting Genbank format to GFF3 format?

[Pierre Lindenbaum]

Hello Dan!

It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/853

This is typically not recommended as it runs the risk of annoying people in both communities.

[Devon Ryan]

Please limit cross-posting both here and on bioinformatics.stackexchange.com, it's a bit of a waste for people to reply in parallel at both places.

Answer 1

[Dan]

Ha, turns out you can just grab the GFF3 from the NCBI's FTP site!

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/003/195/GCA_000003195.3_Sorghum_bicolor_NCBIv3/

See:

• https://www.ncbi.nlm.nih.gov/genome/doc/ftpfaq/#files

Or "Access the data" on the right here:

• https://www.ncbi.nlm.nih.gov/assembly/GCF_000003195.3